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Identification of reliable QTLs and designed QTL breeding for grain shape and milling quality in the reciprocal introgression lines in rice.

ABSTRACT: Milling quality (MQ) and grain shape (GS) of rice (Oryza sativa L.) are correlated traits, both determine farmers' final profit. More than one population under multiple environments may provide valuable information for breeding selection on these MQ-GS correlations. However, suitable analytical methods for reciprocal introgression lines with linkage map for this kind of correlation remains unclear. In this study, our major tasks were (1) to provide a set of reciprocal introgression lines (composed of two BC₂RIL populations) suitable for mapping by linkage mapping using markers/bins with physical positions; (2) to test the mapping effects of different methods by using MQ-GS correlation dissection as sample case; (3) to perform genetic and breeding simulation on pyramiding favorite alleles of QTLs for representative MQ-GS traits. Finally, with four analysis methods and data collected under five environments, we identified about 28.4 loci on average for MQ-GS traits. Notably, 52.3% of these loci were commonly detected by different methods and eight loci were novel. There were also nine regions harboring loci for different MQ-GS traits which may be underlying the MQ-GS correlations. Background independent (BI) loci were also found for each MQ and GS trait. All these information may provide useful resources for rice molecular breeding.

SUBMITTER: Emelin M

PROVIDER: S-EPMC10775519 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature

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Identification of reliable QTLs and designed QTL breeding for grain shape and milling quality in the reciprocal introgression lines in rice.

Emelin Mwenda M Qiu Xianjin X Fan Fangjun F Alamin Md M Faruquee Muhiuddin M Hu Hui H Xu Junying J Yang Jie J Xu Haiming H Ali Jauhar J Liu Bailong B Shi Yumin Y Li Zhikang Z Zhang Luyan L Zheng Tianqing T Xu Jianlong J

BMC plant biology 20240109 1

Milling quality (MQ) and grain shape (GS) of rice (Oryza sativa L.) are correlated traits, both determine farmers' final profit. More than one population under multiple environments may provide valuable information for breeding selection on these MQ-GS correlations. However, suitable analytical methods for reciprocal introgression lines with linkage map for this kind of correlation remains unclear. In this study, our major tasks were (1) to provide a set of reciprocal introgression lines (compos ...[more]

PMID: 38191321

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Project description:IntroductionValidations of previously detected quantitative trait loci (QTLs) to assess their reliability are crucial before implementing breeding programs. The objective of this study was to determine the reliability and practical usefulness of previously reported QTLs for resistance to stem tunneling by the Mediterranean stem borer (MSB) and yield. These authors used approximately 600 recombinant inbred lines (RILs) from a multiparent advanced generation intercross (MAGIC) population to map QTL using a genome-wide association study (GWAS) approach.MethodsWe identified RILs situated at the extremes of resistance and yield distributions within the whole MAGIC, and those QTLs were evaluated per se and crossed to a tester (A638) using lattice designs. In each set, a significant single-nucleotide polymorphism (SNP) was considered validated if (1) the same SNP was associated with the trait with a p-value < 0.02, or (2) within a ±2-Mbp interval, an SNP associated with the trait exhibited a p-value < 0.02 and demonstrated linkage disequilibrium (r2 > 0.2) with the SNPs previously reported.Results and discussionThe novel QTL validation approach was implemented using improved experimental designs that led to higher heritability estimates for both traits compared to those estimated with the whole MAGIC population. The procedure used allowed us to jointly validate several QTL and to ascertain their possible contribution to hybrid improvement. Specifically, nearly three-quarters of the QTLs for tunnel length were confirmed. Notably, QTLs located in the genomic region 6.05-6.07 were consistently validated across different sets and have been previously linked to resistance against stalk tunneling in various mapping populations. For grain yield, approximately 10 out of 16 QTLs were validated. The validation rate for yield was lower than for tunnel length, likely due to the influence of dominance and/or epistatic effects. Overall, 9 out of 21 QTLs for tunnel length and 6 out of 17 QTLs for grain yield identified in our previous research were validated across both validation sets, indicating a moderate genetic correlation between per se and testcross performance of inbred lines. These findings offer insights into the reliability of QTL and genomic predictions, both derived from assessments conducted on the entire MAGIC population. Genomic predictions for tunnel length based on inbred line evaluations could be useful to develop more resistant hybrids; meanwhile, genomic prediction for yield could only be valid in a homozygous background.

Project description:Drought is a major abiotic stress impeding the yield of cereal crops globally. Particularly in Mediterranean environments, water becomes a limiting factor during the reproductive developmental stage, causing yield losses. The wild progenitor of cultivated barley Hordeum vulgare ssp spontaneum (Hsp) is a potentially useful source of drought tolerance alleles. Wild barley introgression lines like the S42IL library may facilitate the introduction of favorable exotic alleles into breeding material. The complete set of 83 S42ILs was genotyped with the barley 9k iSelect platform in order to complete genetic information obtained in previous studies. The new map comprises 2,487 SNPs, spanning 989.8 cM and covering 94.5% of the Hsp genome. Extent and positions of introgressions were confirmed and new information for ten additional S42ILs was collected. A subset of 49 S42ILs was evaluated for drought response in four greenhouse experiments. Plants were grown under well-watered conditions until ten days post anthesis. Subsequently drought treatment was applied by reducing the available water. Several morphological and harvest parameters were evaluated. Under drought treatment, trait performance was reduced. However, there was no interaction effect between genotype and treatment, indicating that genotypes, which performed best under control treatment, also performed best under drought treatment. In total, 40 QTL for seven traits were detected in this study. For instance, favorable Hsp effects were found for thousand grain weight (TGW) and number of grains per ear under drought stress. In particular, line S42IL-121 is a promising candidate for breeding improved malting cultivars, displaying a TGW, which was increased by 17% under terminal drought stress due to the presence of an unknown wild barley QTL allele on chromosome 4H. The introgression line showed a similar advantage in previous field experiments and in greenhouse experiments under early drought stress. We, thus, recommend using S42IL-121 in barley breeding programs to enhance terminal drought tolerance.

Project description:BACKGROUND:High yielding rice varieties are usually low in grain iron (Fe) and zinc (Zn) content. These two micronutrients are involved in many enzymatic activities, lack of which cause many disorders in human body. Bio-fortification is a cheaper and easier way to improve the content of these nutrients in rice grain. RESULTS:A population panel was prepared representing all the phenotypic classes for grain Fe-Zn content from 485 germplasm lines. The panel was studied for genetic diversity, population structure and association mapping of grain Fe-Zn content in the milled rice. The population showed linkage disequilibrium showing deviation of Hardy-Weinberg's expectation for Fe-Zn content in rice. Population structure at K = 3 categorized the panel population into distinct sub-populations corroborating with their grain Fe-Zn content. STRUCTURE analysis revealed a common primary ancestor for each sub-population. Novel quantitative trait loci (QTLs) namely qFe3.3 and qFe7.3 for grain Fe and qZn2.2, qZn8.3 and qZn12.3 for Zn content were detected using association mapping. Four QTLs, namely qFe3.3, qFe7.3, qFe8.1 and qFe12.2 for grain Fe content were detected to be co-localized with qZn3.1, qZn7, qZn8.3 and qZn12.3 QTLs controlling grain Zn content, respectively. Additionally, some Fe-Zn controlling QTLs were co-localized with the yield component QTLs, qTBGW, OsSPL14 and qPN. The QTLs qFe1.1, qFe3.1, qFe5.1, qFe7.1, qFe8.1, qZn6, qZn7 and gRMm9-1 for grain Fe-Zn content reported in earlier studies were validated in this study. CONCLUSION:Novel QTLs, qFe3.3 and qFe7.3 for grain Fe and qZn2.2, qZn8.3 and qZn12.3 for Zn content were detected for these two traits. Four Fe-Zn controlling QTLs and few yield component QTLs were detected to be co-localized. The QTLs, qFe1.1, qFe3.1, qFe5.1, qFe7.1, qFe8.1, qFe3.3, qFe7.3, qZn6, qZn7, qZn2.2, qZn8.3 and qZn12.3 will be useful for biofortification of the micronutrients. Simultaneous enhancement of Fe-Zn content may be possible with yield component traits in rice.

Dataset Information

Identification of reliable QTLs and designed QTL breeding for grain shape and milling quality in the reciprocal introgression lines in rice.

Publications

Identification of reliable QTLs and designed QTL breeding for grain shape and milling quality in the reciprocal introgression lines in rice.

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